Shortly after Black Friday in 2015, people began getting sick with an unknown illness. The symptoms were initially mildly severe so that doctors and hospitals took it for a more serious version of the swine flu. When people began dying around the U.S., they began studying the virus and realized it was smallpox. They distributed the smallpox vaccine and thought things would get better, but they worsened.
In New York
In New York City, authority to maintain order and solve the crisis was initially given to the local hospitals and the New York Police Department. When it became apparent that order was not being maintained and people were being infected in large numbers due to the disorganization of the NYPD and hospitals, the National Guard, Army and Marine Reserves, and the CDC were called in by New York's governor to assist the containment efforts.
Their solution was simple. Quarantine all known infected individuals in the center of the city to keep them away from healthy citizens, and so they could be easily treated. Eventually, the citizenry and sickness scratching at both the National Guard's and the NYPD's numbers lead to them combining their efforts and operations. From then on, they were known as the Joint Task Force, or JTF. Other public authorities such as crossing guards, firefighters, and paramedics were also included in their numbers. On occasion, the Last Man Battalion, or LMB, a PMC hired to protect corporate interests in NYC, would assist JTF efforts to quarantine the sick, though often through brutal methods of punishment. For example, an LMB soldier executed a citizen who defecated in the river.
Eventually, the situation became worse than the JTF could handle. To start with, a lot of manpower had gotten sick and died, leaving them severely undermanned. Secondly, the LMB and JTF cut ties and began carving out parts of the city for themselves, with the LMB forces taking most of the eastern parts of the city. And making matters worse, prisoners had escaped from Rikers Island, killed the few guards remaining and took police equipment, leaving them in control of the southern part of the city. The sanitation workers who had worked to keep the city free of infection and a lot of whom had lost loved ones by bringing the virus into their homes were abandoned in the northeastern part of the city by the JTF, and began torching everything to eliminate the virus with fire.
The Dark Zone
With all that was occurring, the JTF was forced to abandon the quarantine zone and the Division agents assisting them in keeping order. This created a schism between the government and the First Wave of Division, who abandoned their mission of operating as the government's agents and instead sought to take control of the decaying city from the JTF and anyone else.
After pulling out (and abandoning a lot of valuable equipment in the process), the undermanned and outgunned JTF were at the mercy of the escaped prisoners (calling themselves "Rikers") the souped up sanitation workers with flamethrowers (the "Cleaners") and the LMB. They were eventually pushed back to the port in the southwestern part of the city, while the rest of the city was at the mercy of rioters and gangs that had taken advantage of the crisis.
Around the United States
According to Rick Valassi, government assessments have determined that the nationwide infection rate is critical and several major cities are under martial law. Like New York, they are experiencing difficulty with coordinating proper resources and help to those in need. Cities mentioned include Houston, Detroit, Pittsburgh, Boston, Philadelphia, Chicago, Atlanta, San Francisco, and Los Angeles.